Extract all the files in the OpenMW-smm.zip into your C:\Users\[username]\Documents\My Games\OpenMW directory

Put all of your mods folders into the C:\Users\[username]\Documents\My Games\OpenMW\mods directory

Finally just run openmw-smm.exe

You can also add a "-" to the start of a mod directory to make the program ignore it.

Note that this preserves your load order. Also note that this will remove folders that you deleted from your openmw.cfg but it wont(!) disable the mods.
Also you should clear all of your custom mod directories before running this for the first time